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Table 3 Comparisons of call rates and accuracy on HapMap samples for three SNP groups

From: A new model calling procedure for Illumina BeadArray data

Class Prop Item GenCall GenoSNP M-D
g 1 88.60 % Call rate 96.59 99.13 99.77
   Accuracy 96.40 98.44 99.31
g 2 4.03 % Call rate 97.62 99.56 99.75
   Accuracy 97.53 99.45 99.59
g 3 7.37 % Call rate 96.60 99.14 99.70
   Accuracy 96.45 98.71 99.40
  1. Note: M-D: a new model calling procedure; Call rate: the percentage of valid genotypes; Accuracy: the percentage of consistent genotype between each calling method and the gold standard; Class: indicates the three SNPs categories, such as: g 1, g 2 and g 3; Prop: indicates the percentage of SNPs which belong to three groups, respectively